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package Bio::FeatureIO::chado;
use strict;
use base qw(Bio::FeatureIO);
use Bio::SeqIO;
use Bio::Chado::LoadDBI;
use Data::Dumper;
sub _initialize {
my($self,%arg) = @_;
$self->SUPER::_initialize(%arg);
$self->feature_count(0);
$self->organism($arg{-organism} || 'Human');
$self->cachesize($arg{-cachesize} || 1000);
}
sub next_feature {
shift->throw('this class only writes to database');
}
sub write_feature {
my($self,$feature) = shift;
}
=head2 cache
Title : cache
Usage : $obj->cache($newval)
Function: cache an object for commit to db. when number of
items in cache exceeds cachesize(), objects are flushed
Example :
Returns : value of cache (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub cache{
my $self = shift;
my $val = shift;
push @{ $self->{'cache'} }, $val if ref($val);
if(scalar @{ $self->{'cache'} } > $self->cachesize){
$_->dbi_commit foreach @{ $self->{'cache'} };
@{ $self->{'cache'} } = ();
}
}
=head2 cachesize
Title : cachesize
Usage : $obj->cachesize($newval)
Function: number of features to cache before flushing to db
Example :
Returns : value of cachesize (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub cachesize{
my $self = shift;
return $self->{'cachesize'} = shift if @_;
return $self->{'cachesize'};
}
=head2 organism
Title : organism
Usage : $obj->organism($newval)
Function: organism of features being loaded
Example :
Returns : value of organism (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub organism{
my $self = shift;
return $self->{'organism'} = shift if @_;
return $self->{'organism'};
}
1;
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